Sun Oct 9 11:43:50 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 11:43:50 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2688 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6584910 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -6.158000 47.73900 ymin,ymax (A): 8.976001 59.76900 zmin,zma (A): 5.298000 59.36100 x,y,z range (A): 53.89700 50.79300 54.06300 scale (grids/A): 0.6584910 object centre (A): 20.79050 34.37250 32.32950 number of atom coordinates read : 2688 total number of charged atoms : 2620 net assigned charge : 2.000011 assigned positive charge : 402.3631 centred at (gu) : 90.83054 90.23077 91.00706 assigned negative charge : -400.3647 centred at (gu) : 90.85864 90.18127 91.00594 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8354 nv = 96 ne = 84 npr = 50849 no. pairs analyzed = 50849 no. exposed pairs = 3789 no. arc points = 26998 no. surface atoms = 1264 nbur = 1424 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 576 mr = 4336 m= 4 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2100000 number of dielectric boundary points 4526 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2499 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9636 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8250803E-09 6.2777148E-09 midg,1,midg; midg,igrid,midg -4.6134168E-09 1.5269105E-08 1,midg,midg; igrid,midg,midg 8.7553156E-09 -8.1126861E-10 gauss-seidel spectral radius is 0.9880776 estimated iterations to convergence 75 setup time was (sec) 0.4000000 now iterating at: 11:43:51 rms-change max change #iterations 0.1661806 21.83144 at 10iterations 1.7638773E-02 2.466150 at 20iterations 1.8795761E-03 0.2464294 at 30iterations 2.2070736E-04 3.0362606E-02 at 40iterations 5.0602885E-05 8.9101791E-03 at 50iterations finished qdiffx linear iterations at : 11:43:54 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 5.0602885E-05 8.9101791E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 11:43:54 3.422u 0.180s 0:03.87 93.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 11:43:54 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2688 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.975473 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -6.158000 47.73900 ymin,ymax (A): 8.976001 59.76900 zmin,zma (A): 5.298000 59.36100 x,y,z range (A): 53.89700 50.79300 54.06300 scale (grids/A): 1.975473 object centre (A): 20.79050 34.37250 32.32950 number of atom coordinates read : 2688 total number of charged atoms : 2620 net assigned charge : 2.000011 assigned positive charge : 402.3631 centred at (gu) : 92.49061 90.69124 93.02015 assigned negative charge : -400.3647 centred at (gu) : 92.57599 90.54379 93.01765 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 88918 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26998 grid for indexing accessible points = 1.400000 m= 33379 mr = 59208 m= 6539 mr = 24020 m= 556 mr = 4154 m= 9 mr = 215 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 41804 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 20744 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6584910 object centre at (A) : 20.79050 34.37250 32.32950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5181721E-03 3.0805824E-02 midg,1,midg; midg,igrid,midg -5.7006003E-03 2.9119518E-02 1,midg,midg; igrid,midg,midg -1.7962573E-02 -9.9918535E-03 gauss-seidel spectral radius is 0.9987680 estimated iterations to convergence 226 setup time was (sec) 0.6700000 now iterating at: 11:43:55 rms-change max change #iterations 4.684969 182.7017 at 10iterations 2.272655 79.77312 at 20iterations 1.101733 33.16528 at 30iterations 0.5350478 16.07240 at 40iterations 0.2591655 7.798440 at 50iterations 0.1260350 3.665154 at 60iterations 6.1125048E-02 1.828984 at 70iterations 2.9657399E-02 0.9784503 at 80iterations 1.4430111E-02 0.3893280 at 90iterations 7.0033586E-03 0.2163448 at 100iterations 3.3999174E-03 9.7604752E-02 at 110iterations 1.6598711E-03 4.7223091E-02 at 120iterations finished qdiffx linear iterations at : 11:44:02 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 1.6598711E-03 4.7223091E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 11:44:03 8.036u 0.191s 0:08.53 96.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 11:44:03 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2688 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.963210 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -6.158000 47.73900 ymin,ymax (A): 8.976001 59.76900 zmin,zma (A): 5.298000 59.36100 x,y,z range (A): 53.89700 50.79300 54.06300 scale (grids/A): 2.963210 object centre (A): 20.79050 34.37250 32.32950 number of atom coordinates read : 2688 total number of charged atoms : 2620 net assigned charge : 2.000011 assigned positive charge : 402.3631 centred at (gu) : 93.73566 91.03671 94.53014 assigned negative charge : -400.3647 centred at (gu) : 93.86400 90.81570 94.52637 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 205083 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26998 grid for indexing accessible points = 1.400000 m= 103881 mr = 144166 m= 41860 mr = 82987 m= 12086 mr = 33168 m= 2133 mr = 9095 m= 161 mr = 1425 m= 3 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.6800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.150000 number of dielectric boundary points 94297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 20960 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.975473 object centre at (A) : 20.79050 34.37250 32.32950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3006144E-03 0.3755983 midg,1,midg; midg,igrid,midg 2.3320545E-02 0.3182246 1,midg,midg; igrid,midg,midg -0.2365703 0.1465670 gauss-seidel spectral radius is 0.9993184 estimated iterations to convergence 302 setup time was (sec) 1.400000 now iterating at: 11:44:04 rms-change max change #iterations 10.98637 449.2257 at 10iterations 6.663298 158.5957 at 20iterations 4.017997 80.79089 at 30iterations 2.411037 47.26901 at 40iterations 1.443562 31.15540 at 50iterations 0.8592086 14.87504 at 60iterations 0.5104970 9.354248 at 70iterations 0.3029946 6.406533 at 80iterations 0.1789976 3.136424 at 90iterations 0.1058659 1.870346 at 100iterations 6.2555477E-02 1.070465 at 110iterations 3.6938943E-02 0.6875839 at 120iterations 2.1765064E-02 0.3785896 at 130iterations 1.2865127E-02 0.2294846 at 140iterations 7.5930664E-03 0.1291962 at 150iterations 4.5026965E-03 7.9169273E-02 at 160iterations 2.6728236E-03 4.5317411E-02 at 170iterations 1.6100853E-03 2.8698921E-02 at 180iterations finished qdiffx linear iterations at : 11:44:16 total time elapsed so far: 13.20000 # loops : 180 mean,max change (kT/e) : 1.6100853E-03 2.8698921E-02 energy calculations done at 13.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 11:44:17 13.330u 0.202s 0:13.85 97.6% 0+0k 0+0io 0pf+0w